I just bought an e90 and it currently has full exhaust, intercooler, dci, and GIAC stage 2 tune. The CPO warranty runs out in January and I had been planning on taking it in to the dealer to get everything checked out before it expires.

UPDATE
I just had the half engine light come on (it went away on restart) and I do have a BT cable but do not have a PC which I can read the codes.

To get to the point, I want to take it in to the dealer but I would prefer not to remove the mods if necessary. I will put it back to the stock tune and could potentially change the intercooler, intake and downpipes if needed (I dont have the catback exhaust). Any recommendations would be greatly appreciated.

I am picking up a friends laptop tomorrow to scan the code/s, hopefully its just a boost leak. No matter what it is though I decided I want to get the fuel pumps and injectors checked out one more time before the CPO is up so any SA or dealer recommendations would be a huge help.

The DPs will have to come out, along with the tune, and probably intercooler. The most important thing is the tune and DPs: those are a no-go for CPO work. But I would recommend removing everything just to be sure. It's a PITA, but there's a risk that if you go with some mods, a marker will be placed on your VIN and uploaded to the BMW mothership, and then your warranty is done forever. We swap that stuff pretty reasonably and keep stock 'loaner' parts at the shop.